I think the biggest counterargument (if one were needed) is that if I start doing things to your brain, it affects your mind. If I cut a part of your brain out, your mind is impacted. This has been shown by injuries to the brain, lobotomies, etc. etc.
Beyond that, we could get into all sorts of philosophical arguments about the link between the mind and the brain, but it seems to me as a somewhat philosophically naive person that this fact is a clear and demonstrable link between the brain and the mind.
I think no one here assumes Chopra speaks with any authority as to the physiology of the brain. Yes, he's a doctor - of internal medicine with a specialism in endocrinology, but that hardly qualifies him to discuss the brain. That being said, I think the key to understanding the brain physically is to read this book:
An Anatomy of Thought: The Origin and Machinery of the Mind
by Ian Glynn
And to understand the inner workings of the brain and how it theoretically functions:
Society of Mind
by Marvin Lee Minsky
I believe the idea that the mind is just a "set of agents" is best explained in "Society of Mind".
Beyond that, we could get into all sorts of philosophical arguments about the link between the mind and the brain, but it seems to me as a somewhat philosophically naive person that this fact is a clear and demonstrable link between the brain and the mind.